CPPTRAJ: Trajectory Analysis. V15.00 ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Date/time: 11/18/15 22:16:14 | Available memory: 52170.9 MB INPUT: Reading Input from file pt-criteria.in [parm ../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr [traj]] Reading '../../../tip3p/ff12sb/run1/build/noWAt.topo.hmr' as Amber Topology [strip :WAT,Na+,Cl-] STRIP: Stripping atoms in mask [:WAT,Na+,Cl-] [autoimage origin] AUTOIMAGE: To origin based on center of mass, anchor is first molecule. [trajin ../ctraj.c5] Reading '../ctraj.c5' as Amber NetCDF [rmsd :1,2&!@H= first] RMSD: (:1,2&!@H*), reference is first frame (:1,2&!@H*), with fitting. [nativecontacts :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Warning: No reference structure specified. Defaulting to first. NATIVECONTACTS: Mask1=':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Mask2=':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9', contacts set up based on first frame. Distance cutoff is 7 Angstroms, imaging is on. Mask selection will not include solvent. Data set name: Contacts_00001 Saving minimum observed distances in set 'Contacts_00001[mindist]' Contact stats will be written to 'STDOUT' Contact res pairs will be written to 'STDOUT' [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] DISTANCE: :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9, center of mass. [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] VECTOR: Type CorrPlane, mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] VECTORMATH: Calculating Angle from dot product of vectors v_base1 and v_base2 Vectors will be normalized. [run] ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES: 0: [traj] 'noWAt.topo.hmr', 65 atoms, 2 res, box: Orthogonal, 1 mol, 39809 frames INPUT TRAJECTORIES: 0: 'ctraj.c5' is a NetCDF AMBER trajectory, Parm [traj] (Orthogonal box) (reading 39809 of 39809) Coordinate processing will occur on 39809 frames. TIME: Run Initialization took 0.0000 seconds. BEGIN TRAJECTORY PROCESSING: ..................................................... ACTION SETUP FOR PARM '[traj]' (7 actions): 0: [strip :WAT,Na+,Cl-] Stripping 0 atoms. Warning: No atoms to strip. Skipping 'strip' for topology '[traj]' Warning: Setup failed for [strip :WAT,Na+,Cl-]: Skipping 1: [autoimage origin] Anchor molecule is 1 0 molecules are mobile. 2: [rmsd :1,2&!@H= first] Target mask: [:1,2&!@H*](41) Reference mask: [:1,2&!@H*](41) Warning: Coordinates are being rotated and box coordinates are present. Warning: Unit cell vectors are NOT rotated; imaging will not be possible Warning: after the RMS-fit is performed. 3: [nativecontacts :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 mindist] Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 10 potential contact sites for ':1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' 10 potential contact sites for ':2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9' Imaging enabled. 4: [distance COM :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9] :1@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms) to :2@N1,C2,H2,N3,C4,C5,C6,N6,H61,H62,N7,C8,H8,N9 (14 atoms), imaged. 5: [vector v_base1 :1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Vector mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. 6: [vector v_base2 :2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9 corrplane] Vector mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. ----- ctraj.c5 (1-39809, 1) ----- 0% Using first frame to determine native contacts. Mask [:1@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Mask [:2@N1,C2,N3,C4,C5,C6,N6,N7,C8,N9] corresponds to 10 atoms. Setup 39 native contacts: Atom ':1@C6' to ':2@C6' Atom ':1@C6' to ':2@N6' Atom ':1@C6' to ':2@N1' Atom ':1@C6' to ':2@C2' Atom ':1@N1' to ':2@N9' Atom ':1@N1' to ':2@C8' Atom ':1@N1' to ':2@N7' Atom ':1@N1' to ':2@C5' Atom ':1@N1' to ':2@C6' Atom ':1@N1' to ':2@N6' Atom ':1@N1' to ':2@N1' Atom ':1@N1' to ':2@C2' Atom ':1@N1' to ':2@N3' Atom ':1@N1' to ':2@C4' Atom ':1@C2' to ':2@N9' Atom ':1@C2' to ':2@C8' Atom ':1@C2' to ':2@N7' Atom ':1@C2' to ':2@C5' Atom ':1@C2' to ':2@C6' Atom ':1@C2' to ':2@N6' Atom ':1@C2' to ':2@N1' Atom ':1@C2' to ':2@C2' Atom ':1@C2' to ':2@N3' Atom ':1@C2' to ':2@C4' Atom ':1@N3' to ':2@N9' Atom ':1@N3' to ':2@C8' Atom ':1@N3' to ':2@N7' Atom ':1@N3' to ':2@C5' Atom ':1@N3' to ':2@C6' Atom ':1@N3' to ':2@N6' Atom ':1@N3' to ':2@N1' Atom ':1@N3' to ':2@C2' Atom ':1@N3' to ':2@N3' Atom ':1@N3' to ':2@C4' Atom ':1@C4' to ':2@N9' Atom ':1@C4' to ':2@N7' Atom ':1@C4' to ':2@C5' Atom ':1@C4' to ':2@C6' Atom ':1@C4' to ':2@C4' 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% Complete. Read 39809 frames and processed 39809 frames. TIME: Trajectory processing: 0.2089 s TIME: Avg. throughput= 190585.8472 frames / second. ACTION OUTPUT: CONTACTS: Contacts_00001 #Res1 #Res2 TotalFrac Contacts 1 2 5.17059 39 # Contact Nframes Frac. Avg Stdev 1 :1@N3_:2@N9 15597 0.392 6.24 0.536 2 :1@C2_:2@N9 14565 0.366 6.14 0.62 3 :1@N3_:2@C8 13812 0.347 6.12 0.824 4 :1@C2_:2@C8 11158 0.28 6.02 0.918 5 :1@C4_:2@N9 11014 0.277 6.46 0.372 6 :1@N1_:2@N9 10989 0.276 6.4 0.502 7 :1@C2_:2@C4 7994 0.201 6.2 0.66 8 :1@N3_:2@C4 7137 0.179 6.35 0.501 9 :1@N1_:2@C8 7099 0.178 6.13 0.793 10 :1@N3_:2@N7 6731 0.169 6.04 0.966 11 :1@C2_:2@N3 6501 0.163 6.13 0.749 12 :1@C2_:2@N7 5900 0.148 5.86 1.14 13 :1@N1_:2@C4 5602 0.141 6.31 0.57 14 :1@C4_:2@N7 5489 0.138 6.23 0.697 15 :1@N3_:2@N3 5411 0.136 6.26 0.641 16 :1@N1_:2@N3 5177 0.13 6.19 0.696 17 :1@C2_:2@C5 4729 0.119 6.01 0.858 18 :1@N3_:2@C5 4622 0.116 6.22 0.637 19 :1@C4_:2@C4 4146 0.104 6.68 0.264 20 :1@C2_:2@C2 4074 0.102 6.12 0.812 21 :1@N1_:2@N7 4064 0.102 5.85 1.02 22 :1@N1_:2@C5 3484 0.0875 6.05 0.744 23 :1@N1_:2@C2 3319 0.0834 6.16 0.778 24 :1@C2_:2@C6 3211 0.0807 6.08 0.674 25 :1@N3_:2@C2 3153 0.0792 6.13 0.768 26 :1@C2_:2@N1 2897 0.0728 6.17 0.694 27 :1@N3_:2@C6 2871 0.0721 6.35 0.467 28 :1@C4_:2@C5 2773 0.0697 6.54 0.356 29 :1@N1_:2@C6 2626 0.066 6.12 0.636 30 :1@C2_:2@N6 2479 0.0623 6.08 0.717 31 :1@N1_:2@N1 2447 0.0615 6.25 0.653 32 :1@C6_:2@C2 2302 0.0578 6.34 0.604 33 :1@N1_:2@N6 2187 0.0549 6.02 0.758 34 :1@N3_:2@N1 2040 0.0512 6.18 0.669 35 :1@N3_:2@N6 1981 0.0498 6.35 0.51 36 :1@C6_:2@C6 1843 0.0463 6.49 0.391 37 :1@C6_:2@N6 1693 0.0425 6.29 0.545 38 :1@C6_:2@N1 1406 0.0353 6.43 0.497 39 :1@C4_:2@C6 1313 0.033 6.64 0.304 ANALYSIS: Performing 1 analyses: 0: [vectormath name normalangle vec1 v_base1 vec2 v_base2 dotangle] TIME: Analyses took 0.0018 seconds. DATASETS: 8 data sets: RMSD_00000 "RMSD_00000" (double, rms), size is 39809 Contacts_00001[native] "Contacts_00001[native]" (integer), size is 39809 Contacts_00001[nonnative] "Contacts_00001[nonnative]" (integer), size is 39809 Contacts_00001[mindist] "Contacts_00001[mindist]" (double), size is 39809 COM "COM" (double, distance), size is 39809 v_base1 "v_base1" (vector), size is 39809 v_base2 "v_base2" (vector), size is 39809 normalangle "normalangle" (double), size is 39809 DATAFILES: STDOUT (Native Contacts) STDOUT (Contact Res Pairs) ---------- RUN END --------------------------------------------------- [writedata criteria-raw.dat Contacts_00001[mindist] COM normalangle] Writing sets to criteria-raw.dat, format 'Standard Data File' Contacts_00001[mindist] COM normalangle TIME: Total execution time: 0.3118 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095.